Detailed analyses using multiple sequence alignments and phylogenetic reconstructions were carried out to assign putative functions to the ORFs, when needed.
One of the major benefits of these DNA barcodes was the ability to rapidly provide an accurate F/B ratio from a pool of thousands of short sequencing reads generated by the pyrosequencing method, without the need to assemble sequences, perform multiple sequence alignments, generate phylogenetic reconstructions, or perform BLAST analyses.
Final alignments were used in phylogenetic reconstructions through multiple programs available in the Phylogeny Inference Package - PHYLIP, version 3.69 [ 31].
FIGENIX allows sequences retrieval, multiple sequence alignments, phylogenetic reconstruction and orthology and paralogy relationships deductions.
The FIGENIX platform retrieved sequences, provided multiple sequence alignments, phylogenetic reconstruction and deduced orthology and paralogy relationships (for a detailed description of pipelines and models used, see [ 46]).
First, this method generates high quality multiple sequence alignments that can be used for phylogenetic reconstructions as well as for diversity measures such as the identification of OTUs.
Multiple sequence alignments were made using ClustalW [134], and phylogenetic reconstructions were made using SplitsTree [135].
Multiple alignments were attained by using ClustalW (19 ) For phylogenetic reconstructions, we retrieved complete and partial RABV sequences from GenBank that represented historical and ongoing rabies epizootics in the Americas (Technical Appendix Table 2).
Genome-scale comparisons between multiple crustacean and other arthropod taxa may more accurately resolve the phylogenetic reconstructions between crustacean and hexapod arthropoda based on a small number of nuclear loci or in mitochondrial genomes, which are only maternally inherited.
The accession numbers of the sequences utilized in the phylogenetic reconstructions are listed in Additional file 4. Multiple sequence alignments were performed using MUSCLE version 3.8 [ 78] and CLUSTALW (built into the MEGA 4 software) [ 79].
